Alignments for a candidate for hcs in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Rhodospirillum rubrum ATCC 11170

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate YP_427356.1 Rru_A2269 pyruvate carboxyltransferase

Query= SwissProt::P05342
         (385 letters)



>NCBI__GCF_000013085.1:YP_427356.1
          Length = 392

 Score =  384 bits (986), Expect = e-111
 Identities = 199/367 (54%), Positives = 261/367 (71%), Gaps = 1/367 (0%)

Query: 2   ASVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIA 61
           +SVI++DTTLRDGEQ+AGV F   EK+AIA+AL   GVPE+E+GIP+MG EE+E + A+ 
Sbjct: 4   SSVIVNDTTLRDGEQTAGVIFTLGEKVAIAKALERAGVPEMEVGIPAMGPEEQESIRAVV 63

Query: 62  GLGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARLV 121
               +SR +AWCR+   DL AA + GV MV+LS+PVSD  +  KL RDR W L  +  ++
Sbjct: 64  AQCEASRPIAWCRMHMTDLDAAAACGVDMVNLSIPVSDQQIKGKLGRDRGWVLAHLETMI 123

Query: 122 GEARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFRF 181
             A   GLEV LG ED+SRAD EF+++V E A+A+GARR RFADT+G+M+PF  L  F+ 
Sbjct: 124 KTALEKGLEVALGGEDSSRADPEFLLRVIERAEASGARRFRFADTLGIMDPFTTLQMFKR 183

Query: 182 LSRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALKN 241
           L     +ELE+HAHDD GLATAN+L AV+GGATH++TTVNGLGERAGNA LEE V+A +N
Sbjct: 184 LRAASGLELEIHAHDDLGLATANSLGAVLGGATHVSTTVNGLGERAGNAPLEEVVMACRN 243

Query: 242 LHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYEG 301
           L+G  TGI    + A+S LV  ASGR V   K +VG  +FTHE+GIHV GLL+  +NYE 
Sbjct: 244 LYGRHTGIAPMALAAVSKLVAEASGRPVPANKPIVGEAIFTHESGIHVSGLLRDPKNYEA 303

Query: 302 LNPDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRRSPQP 361
           L+P +LGR H LVLGKHSG   + +    LG+   + Q++A+L R+R  +  TK R P  
Sbjct: 304 LSPADLGRCHRLVLGKHSGVASIVHACNALGLAPGEAQARAMLARVRLHAGATK-RPPTD 362

Query: 362 AELQDFY 368
           A+L+ F+
Sbjct: 363 ADLRRFF 369


Lambda     K      H
   0.320    0.135    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 455
Number of extensions: 16
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 385
Length of database: 392
Length adjustment: 30
Effective length of query: 355
Effective length of database: 362
Effective search space:   128510
Effective search space used:   128510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate YP_427356.1 Rru_A2269 (pyruvate carboxyltransferase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR02660.hmm
# target sequence database:        /tmp/gapView.1280.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                              Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   2.2e-160  519.8   0.9   2.5e-160  519.7   0.9    1.0  1  lcl|NCBI__GCF_000013085.1:YP_427356.1  Rru_A2269 pyruvate carboxyltrans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_427356.1  Rru_A2269 pyruvate carboxyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.7   0.9  2.5e-160  2.5e-160       2     364 ..       6     368 ..       5     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 519.7 bits;  conditional E-value: 2.5e-160
                              TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcRl 73 
                                            v++nDttLRDGEq+agv+F+  EK+aiAkaL++aGv+e+EvGipamg eE+++ira++a+ + +r +aWcR+
  lcl|NCBI__GCF_000013085.1:YP_427356.1   6 VIVNDTTLRDGEQTAGVIFTLGEKVAIAKALERAGVPEMEVGIPAMGPEEQESIRAVVAQCEASRPIAWCRM 77 
                                            89********************************************************************** PP

                              TIGR02660  74 raedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeeflv 145
                                            +++d++aaa++Gv++v+ls+pvsd+q++ kl +dr wvl++l++++++a e+gl+v++g+eD+sRad+efl 
  lcl|NCBI__GCF_000013085.1:YP_427356.1  78 HMTDLDAAAACGVDMVNLSIPVSDQQIKGKLGRDRGWVLAHLETMIKTALEKGLEVALGGEDSSRADPEFLL 149
                                            ************************************************************************ PP

                              TIGR02660 146 elaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsvt 217
                                            +++e a+++ga+R+RfaDt+g++dPf+t++++k+lraa+ lelE+HaH+DlGlAtAn+l av +Ga++vs+t
  lcl|NCBI__GCF_000013085.1:YP_427356.1 150 RVIERAEASGARRFRFADTLGIMDPFTTLQMFKRLRAASGLELEIHAHDDLGLATANSLGAVLGGATHVSTT 221
                                            ************************************************************************ PP

                              TIGR02660 218 vlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdg 289
                                            v+GlGERAGnA+leev++a ++l+g++tgi   +l ++s+lva+asgr+++a+k++vGe++F+HEsGiHv+g
  lcl|NCBI__GCF_000013085.1:YP_427356.1 222 VNGLGERAGNAPLEEVVMACRNLYGRHTGIAPMALAAVSKLVAEASGRPVPANKPIVGEAIFTHESGIHVSG 293
                                            ************************************************************************ PP

                              TIGR02660 290 llkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeel 361
                                            ll+d+++Ye+l+P+ +Gr ++lv+GKHsg a++++a+++lgl+  e++a+++l++vr +a ++Kr++++++l
  lcl|NCBI__GCF_000013085.1:YP_427356.1 294 LLRDPKNYEALSPADLGRCHRLVLGKHSGVASIVHACNALGLAPGEAQARAMLARVRLHAGATKRPPTDADL 365
                                            ************************************************************************ PP

                              TIGR02660 362 aal 364
                                            +++
  lcl|NCBI__GCF_000013085.1:YP_427356.1 366 RRF 368
                                            876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (392 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.42
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis